Bug: Outputting issues with variables in every domain

[bms63]

Look in 84-deepdive branch for data and specs

library(dplyr)
library(xportr)

spec_loc <- here::here("example_data_specs", "TDF_ADaM_Pilot3.xlsx")

var_spec <- readxl::read_xlsx(spec_loc, sheet = "Variables") %>% 
  mutate(Label = if_else(Variable == "TRTSDT", 
                         "Date of First Exposure to Treatment Date of First Exposure to Treatment", Label))

adsl_loc <- here::here("example_data_specs", "adsl.xpt")

adsl <- haven::read_xpt(adsl_loc) %>% 
  metatools::remove_labels() 

adsl_lbl <- xportr_label(adsl, var_spec, "ADSL", verbose = "warn")

Should just be one TRTSDT

If time given, then look into other xportr functions

[averissimo]

This is a problem when the spec has column names in Snake case: Variable instead of variable, as xportr is not case insensitive.

It just assumes there's no domain in the spec, hence appearing multiple times.

I have 3 suggestions:

• Case insensitive search:: either convert everything needed to lowercase or use case insensitive compares
• Guide the user, but keep functionality:: Check if there are duplicate variables in the spec and message/warn for this issue
• Keep it as is

edit: added the 3rd suggestion

[averissimo]

This also risks the functions themselves as it might not be able to find the column with the metadata (example: No label column in xportr_label)

Example of spec file from pilot 3

Default values

[cpiraux]

In addition to the column names case in metadata, we could check the mapping between the metadata and the expected metadata structure.

The column names in the specifications file may differ depending on the template used for the specifications.

It would be valuable to provide guidance to the user regarding which part of the metadata does not align with the expected metadata structure, what is the expected structure, and how to update the metadata to conform to the expected structure.

For instance, in the P21C template, the column name is 'Data Type,' whereas the expected value is 'type.'

[bms63]

I think xportr.options is supposed to allow us to change variable to Variable. I was using this in my vignette, but honestly I find it a little confusing to use.